Hi,
>> > tail fecp2.pm6.sp.out
>> QMMM: System specified with odd number of electrons ( 57)
>> QMMM: but odd spin ( 1). You most likely have the charge of
>> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
>> calculation.
>>
>> then test AT parallel: 37 passed, 0 fail
>
> weird....can you post the entire output file? This one has not been
> reported
> before (should find 58 electrons).
The output only contained this error. But I found that the input file
fecp2.pm6.sp.in does not have a newline after the last atom, apparently
this last hydrogen is not found then and an odd electron number is
obtained. Adding a newline at the end fixes this and the test passes.
Maybe my sqm compile is more strict about newlines?
>> and in qmmm_EXTERN/QMMM_MD_GAUSSIAN the scripts
>>
>> ./Run.aladip.hf_sto-3g
>> ./Run.nma-spcfw-15.hf_sto-3g
>>
>> fail because there is no g09 executable. I have g03 but not g09
>> installed,
>> I'm not sure why it fails instead of skipping the test.
>
> Is g03 in your path? Is g03 in $GAUSS_EXEDIR? If you unset your
> environment
> variable GAUSS_EXEDIR, it should skip the tests. On the other hand, it
> should
> work with either g03 or g09. Look at $AMBERHOME/test/check_GAUSSIAN.x.
g03 is in my PATH and in GAUSS_EXEDIR, therefore check_GAUSSIAN.x returns 0.
But the test still tries to call g09 (which does not exist) and I could
not figure out where in e.g.
amber12/test/qmmm_EXTERN/pure_QM_MD_GAUSSIAN/Run.h2o.blyp_sto-3g
the actual name of the Gaussian executable is set. It looks like it checks
for g03 or g09, but then assumes g09 is installed.
>> also in qmmm_EXTERN/QMMM_MD_Orca ./Run.aladip.hf_sto-3g.MechEm fails and
>> in qmmm_EXTERN/QMMM_MD_TeraChem ./Run.aladip.hf_sto-3g.MechEm and
>> ./Run.nma-spcfw-15.hf_sto-3g.MechEm fail, all three by virtue of not
>> existing.
>
> Can you try to see why the check_Orca.x script is not correctly
> identifying
> that you don't have ORCA installed?
The check script is fine (I dont have Orca), but it isn't even called,
because the test files
qmmm_EXTERN/QMMM_MD_Orca/Run.aladip.hf_sto-3g.MechEm
and
qmmm_EXTERN/QMMM_MD_TeraChem/Run.aladip.hf_sto-3g.MechEm
qmmm_EXTERN/QMMM_MD_TeraChem/Run.nma-spcfw-15.hf_sto-3g.MechEm
do not exist. To me this looks like a test that has been removed but is
still called in the Makefile, or some files are missing in my tarball.
>> Furthermore in amoeba_wat2 test ./Run.ntpverlet.pmemd segfaulted with no
>> output but the 'Amber 11 SANDER...' output file header. huh?
>
> This is known behavior: pmemd.amoeba will fail badly if there is not
> enough
> stack space, but Bob never figured out how to correctly test for this. At
> least the error tells you not to run pmemd.amoeba....We should probably
> add
> a better explanation to the test script.
I reran this one with 400MB stack space and it still segfaulted. If that
is expected, then ok, I guess...
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Apr 02 2012 - 02:30:04 PDT
